A 34-year-old Japanese man was admitted to an outside hospital with an elevated creatinine kinase level and suspected myositis. He was treated with high dose methylprednisolone, which caused severe aggravation of muscle weakness. He was transferred to our hospital at that time. On admission, chest computed tomography (CT) and the presence of anti-acetylcholine receptor antibodies supported a diagnosis of myasthenia gravis and thymoma. Laboratory findings showed hypokalemia, low plasma renin activity and high serum aldosterone. Further studies, including abdominal CT and adrenal venous sampling suggested primary aldosteronism. At first, thymectomy was performed, and one month later, he was treated with laparoscopic adrenalectomy. Immediately after this procedure, he suffered from myasthenic crisis, which was successfully managed with mechanical ventilation and steroid pulse therapy followed by oral prednisolone. This case presented a serious difficulty in differentiating from various myopathies and giving proper treatment because of a rare combination of independent diseases and their masquerading clinical features.